Red-backed shrike geolocator data

Route map

Photo from Wikipedia Commons

Shrikes were songbirds; he ought to know…
— Jodi Meadows

The red-backed shrike (Lanius collurio) is a carnivorous passerine bird and member of the shrike family Laniidae. Its breeding range stretches from Western Europe east to central Russia. It is migratory and winters in the eastern areas of tropical Africa and southern Africa.

Ingest

The routes

routes <- read.csv("archetypes/red-backed-shrike/red-backed-shrike-coords.csv", header = TRUE)
routes

Ingest

The stopovers

stopovers <- read.csv("archetypes/red-backed-shrike/red-backed-shrike-main-stopovers.csv", header = TRUE)
stopovers

Base map

natural earth

ne_world <- ne_countries(scale = "medium", returnclass = "sf")

Map labels

from centroids within range of limits

centroids = read.csv("archetypes/red-backed-shrike//country-centroids.csv", header = TRUE, stringsAsFactors = FALSE, as.is=T)
countryref <- centroids %>% select(iso3c, latitude, longitude)
countryref <- filter(countryref, latitude > -35 & latitude < 60)
countryref <- filter(countryref, longitude > -20 & longitude < 55)

countryref

Route map

follow the shrike

theme_opts <- theme(
      axis.line=element_blank(),
      axis.text.x=element_blank(),
      axis.text.y=element_blank(),
      axis.ticks=element_blank(),
      axis.title.x=element_blank(),
      axis.title.y=element_blank(),
      legend.position="none",
      legend.title = element_blank(),
      panel.grid.major = element_blank(),
      panel.grid.minor = element_blank(),
      panel.background=element_rect(fill="#ffffff", colour="#ffffff"),
      panel.border = element_blank()
)

# color palette for number of months
pal <- wes_palette("Zissou1", 12, type = "continuous")

v1 <- ggplot(data = ne_world) +
  geom_sf(data = ne_world, fill="#f5f5f5", color="#d5d5d5", size=1.0) +
  geom_text(data= countryref, aes(x=longitude, y=latitude, label=iso3c),
            color = "gray20", fontface = "italic", check_overlap = T, size = 2) +
  # routes
  geom_path(data = routes, aes(y, x), alpha = 0.8, size = 1.5, color = "#666666" ) + 
  geom_point(data = routes, aes(y, x), shape=21, alpha = 1.0, size = 2.0, fill = "#ffffff", color = "#666666") +
  # stopovers
  geom_point(data = stopovers, aes(Medianlon, Medianlat, size = stopover_duration, color = Main_month), alpha = 0.9) +
  # Now, for each of these points we plot the uncertainties
  # Horizontal
  geom_segment(data = stopovers, aes(y=Medianlat, x=FstQu.lon, xend=TrdQu.lon, yend=Medianlat), size = 0.5) +
  # Vertical
  geom_segment(data = stopovers, aes(y=FstQu.lat, x=Medianlon, xend=Medianlon, yend=TrdQu.lat), size = 0.5) +
  # color and size scales
  scale_color_gradientn(colours = pal) + 
  scale_size_continuous(range=c(3,12)) +
  # limit view to relevant area
  coord_sf(xlim = c(-20, 55), ylim = c(-35, 60), expand = TRUE) +
  theme_bw() +
  labs(x=NULL,
       y=NULL,
       title = "Red-Backed Shrike", 
       subtitle="Geolocation Routes") +
  theme_opts

girafe(ggobj = v1, width_svg = 1280/72, height_svg = 720/72,
       options = list(opts_sizing(rescale = TRUE, width = 1.0))
)

References

citations for narrative and data sources

Narrative and Data Source:
- Pedersen, Lykke & Thorup, Kasper & Tøttrup, Anders. (2018).
- Annual GPS tracking reveals unexpected wintering area in a long-distance migratory songbird.
- Journal of Ornithology. 160. 10.1007/s10336-018-1610-8.